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Old 11-25-2013, 06:02 AM   #2
trexbob
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Location: Atlanta, GA

Join Date: Feb 2013
Posts: 17
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Hi Sergio,
I'm also relatively new at this also, but... I can help somewhat. The Ion Torrent software usually trims off the 5' adapter, so unless you have a primer, you generally don't have to do 5' trimming. I've found however that there are usually base pairing issues in the first 10 bases or so, similar to thread http://seqanswers.com/forums/showthread.php?t=17521 . You should use FastQC or a similar program to analyze the quality of the sequencing and trim accordingly. You can use fastxtoolkit to trim Ion Torrent data, just be sure to include the parameter -Q 33 at the end to account for the quality score issue.
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